This is all assuming those characters don't manage to get in as either clones or their own unique character and thus it would be nice to at least have them in the game in SOME fashion. Better than not at all!
Zamus - Sheik, Jody Summers, Mrs. Arrow, maybe even Princia Ramode and Lily Flyer if possible
Samus - Dark Samus, etc.
Peach - Daisy (with voice change) and Pauline and maybe even Mona and Ayumi Tachibana (since schoolgirls are so popular)
Zelda - Various Fire Emblem and Golden Sun females
Kirby - Gooey
Any Pokemon - Any Pokemon (ex: Pikachu - Raichu or Mewtwo - Most Bipedal Pokemon)
Yoshi - Birdo (even if it means seeing Yoshi's tongue come out of her snout. They could just make the tongue invisible though but that would give Birdo a gameplay advantage, which costume changes aren't supposed to get)
Bowser - K. Rool, Wart, Blastoise, and Koopa Troopa (....which means we'd get a GIANT Koopa Troopa that breathes fire, lol. ...and a fire breathing Blastoise, come to think about it. Maybe they could edit the fire graphics to be blue or something)
Falcon - Any feasible F-Zero racers (Blood Falcon or Phoenix or Super Arrow for example, but likely not Samurai Goroh or Princia Ramode. I said feasible)
Dedede - Samurai Goroh (...okay, this one's a joke. But boy would THAT be funny)
Fox McCloud - Most other Starfox characters (including James McCloud. Hell, technically, even Krystal could feasibly be a Fox custome change if she came with a voice change too)
Mario - Dr. Mario (duh) and Stanley (the bugman from DK3)
Donkey Kong - Donkey Kong Jr., Kiddie Kong, Swanky Kong, and (one beefed up muscular) Cranky Kong
Diddy - Dixie and Tiny (with voice changes)
Toad - Toadette, Toadsworth, Toadofsky, Toadinurbasekillinurdudes, etc.
Luigi - Luigi with Waluigi head and voice (since a fullbody costume change would likely not be feasible due to differen body shapes. ...this would look really really messed up, but that's part of the fun)
Goomba - Geno (gotta get Geno in there somehow since Goomba beat him in that poll held for Melee)